In practice most pilots use an iPad app for flight planning and navigation. No technical reason why open source hardware/software could be used for that if it had good UX (which is pretty uncommon in the Linux desktop space)
I think you and the link in OP are talking about two different things. The link talks about "safety-critical avionics" and answers mention that they use proprietary RTOS. Certainly, anything that can be done on iPad could be done on Linux, and Linux is quite common for non-real time embedded things.